duncanparkes
commented
7 years ago If #87 could be solved by opening fast5 files from a tar archive without writing them to disk, that would solve this issue too.
I like the idea of using mkdtemp above. Another possibility would be to let poretools take an argument (or look at an environment variable) to decide where to put the temporary directory.
Hello,
I got this error when running poretools twice simultaneously:
OSError: [Errno 39] Directory not empty: '.poretools_tmp/H566_ON_inc'
It would be useful to fix this, and I guess it could be done by using tempfile.mkdtemp, instead of the static name '.poretools_tmp'.
I hope that helps. Have a nice day, Martin Frith
P.S. Full error message:
Traceback (most recent call last): File "/usr/local/bin/poretools", line 9, in
load_entry_point('poretools==0.5.1', 'console_scripts', 'poretools')()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 401, in main
args.func(parser, args)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/poretools_main.py", line 47, in run_subtool
submodule.run(parser, args)
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/fastq.py", line 6, in run
for fast5 in Fast5File.Fast5FileSet(args.files):
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 36, in init
self._extract_fast5_files()
File "/usr/local/lib/python2.7/dist-packages/poretools-0.5.1-py2.7.egg/poretools/Fast5File.py", line 81, in _extract_fast5_files
shutil.rmtree(PORETOOLS_TMPDIR)
File "/usr/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/usr/lib/python2.7/shutil.py", line 256, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/usr/lib/python2.7/shutil.py", line 254, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: '.poretools_tmp/H566_ON_inc'